running dandisets-healthstatus test-files matnwb_nwbRead -- fails
```shell
(venv) (dandisets) dandi@drogon:~/cronlib/dandisets-healthstatus$ dandisets-healthstatus test-files matnwb_nwbRead /mnt/backup/dandi/dandisets-healthstatus/dandisets-fuse/000552/sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb
2023-08-09 09:40:58 [DEBUG ] Starting new HTTPS connection (1): api.github.com:443
2023-08-09 09:40:59 [DEBUG ] https://api.github.com:443 "GET /repos/NeurodataWithoutBorders/matnwb/releases/latest HTTP/1.1" 200 842
2023-08-09 09:40:59 [INFO ] Testing /mnt/backup/dandi/dandisets-healthstatus/dandisets-fuse/000552/sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb ...
2023-08-09 09:40:59 [DEBUG ] Using selector: EpollSelector
Error using assert
Unexpected properties {data_offset}.
Your schema version may be incompatible with the file. Consider checking the
schema version of the file with `util.getSchemaVersion(filename)` and comparing
with the YAML namespace version present in nwb-schema/core/nwb.namespace.yaml
Error in types.util.checkUnset (line 17)
assert(isempty(dropped),...
Error in types.core.SpatialSeries (line 35)
types.util.checkUnset(obj, unique(varargin(1:2:end)));
Error in io.parseGroup (line 85)
parsed = eval([Type.typename '(kwargs{:})']);
Error in io.parseGroup (line 38)
subg = io.parseGroup(filename, group, Blacklist);
Error in io.parseGroup (line 38)
subg = io.parseGroup(filename, group, Blacklist);
Error in io.parseGroup (line 38)
subg = io.parseGroup(filename, group, Blacklist);
Error in io.parseGroup (line 38)
subg = io.parseGroup(filename, group, Blacklist);
Error in nwbRead (line 59)
nwb = io.parseGroup(filename, h5info(filename), Blacklist);
2023-08-09 09:51:00 [INFO ] /mnt/backup/dandi/dandisets-healthstatus/dandisets-fuse/000552/sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb: FAIL
```
but it is not reporting any detail about version of the matnwb or exact invocation of matlab here, making it impossible to reproduce:
I fail to reproduce when I try with the simpler code/checknwb.sh (but note: that one does not use datalad-fuse -- it downloads the file
```shell
(venv) (dandisets) dandi@drogon:~/cronlib/dandisets-healthstatus$ code/checknwb.sh 000552 sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb master v2.6.0.2
/tmp/matnwb-aH0BDuK
Cloning into '000552'...
remote: Enumerating objects: 1040, done.
remote: Counting objects: 100% (1040/1040), done.
remote: Compressing objects: 100% (787/787), done.
remote: Total 1040 (delta 109), reused 1015 (delta 84), pack-reused 0
Receiving objects: 100% (1040/1040), 182.75 KiB | 2.50 MiB/s, done.
Resolving deltas: 100% (109/109), done.
Version of the dandiset:
0.230630.2304-1-gad8452b
Remote origin not usable by git-annex; setting annex-ignore
https://github.com/dandisets/000552/config download failed: Not Found
get sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb (from web...)
ok
(recording state in git...)
Cloning into 'matnwb'...
remote: Enumerating objects: 9328, done.
remote: Counting objects: 100% (2496/2496), done.
remote: Compressing objects: 100% (1019/1019), done.
remote: Total 9328 (delta 1636), reused 2048 (delta 1472), pack-reused 6832
Receiving objects: 100% (9328/9328), 27.51 MiB | 25.24 MiB/s, done.
Resolving deltas: 100% (6007/6007), done.
+ for v in "$@"
+ git checkout master
Already on 'master'
Your branch is up to date with 'origin/master'.
+ echo 'Running using: '
Running using:
+ git describe --tags
v2.6.0.2-11-g286d6b5
+ MATLABPATH=/tmp/matnwb-aH0BDuK/matnwb
+ time matlab -nodesktop -batch 'f='\''../000552/sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb'\''; disp(util.getSchemaVersion(f)); nwb = nwbRead(f)'
2.6.0
nwb =
NwbFile with properties:
nwb_version: '2.6.0'
file_create_date: [1x1 types.untyped.DataStub]
identifier: '19872f12-b3c7-48cb-bc14-f6107c80d9b8'
session_description: 'The incorporation of new information into the hippocampal network is likely to be constrained by its innate architecture and internally generated activity patterns. However, the origin, organization and consequences of such patterns remain poorly understood. In the present study we show that hippocampal network dynamics are affected by sequential neurogenesis. We birthdated CA1 pyramidal neurons with in utero electroporation over 4 embryonic days, encompassing the peak of hippocampal neurogenesis, and compared their functional features in freely moving adult mice. Neurons of the same birthdate displayed distinct connectivity, coactivity across brain states and assembly dynamics. Same-birthdate neurons exhibited overlapping spatial representations, which were maintained across different environments. Overall, the wiring and functional features of CA1 pyramidal neurons reflected a combination of birthdate and the rate of neurogenesis. These observations demonstrate that sequential neurogenesis during embryonic development shapes the preconfigured forms of adult network dynamics.'
session_start_time: 2021-03-19
timestamps_reference_time: 2021-03-19
acquisition: [0x1 types.untyped.Set]
analysis: [0x1 types.untyped.Set]
general: [0x1 types.untyped.Set]
general_data_collection: ''
general_devices: [1x1 types.untyped.Set]
general_experiment_description: 'Preconfigured dynamics in the hippocampus are guided by embryonic birthdate and rate of neurogenesis'
general_experimenter: [1x1 types.untyped.DataStub]
general_extracellular_ephys: [8x1 types.untyped.Set]
general_extracellular_ephys_electrodes: [1x1 types.hdmf_common.DynamicTable]
general_institution: 'Princeton'
general_intracellular_ephys: [0x1 types.untyped.Set]
general_intracellular_ephys_experimental_conditions: []
general_intracellular_ephys_filtering: ''
general_intracellular_ephys_intracellular_recordings: []
general_intracellular_ephys_repetitions: []
general_intracellular_ephys_sequential_recordings: []
general_intracellular_ephys_simultaneous_recordings: []
general_intracellular_ephys_sweep_table: []
general_keywords: [1x1 types.untyped.DataStub]
general_lab: 'Buzsaki'
general_notes: ''
general_optogenetics: [0x1 types.untyped.Set]
general_optophysiology: [0x1 types.untyped.Set]
general_pharmacology: ''
general_protocol: ''
general_related_publications: [1x1 types.untyped.DataStub]
general_session_id: 'e13_16f1_210319'
general_slices: ''
general_source_script: ''
general_source_script_file_name: ''
general_stimulus: ''
general_subject: [1x1 types.core.Subject]
general_surgery: ''
general_virus: ''
intervals: [0x1 types.untyped.Set]
intervals_epochs: [1x1 types.core.TimeIntervals]
intervals_invalid_times: []
intervals_trials: [1x1 types.core.TimeIntervals]
processing: [2x1 types.untyped.Set]
scratch: [0x1 types.untyped.Set]
stimulus_presentation: [0x1 types.untyped.Set]
stimulus_templates: [0x1 types.untyped.Set]
units: [1x1 types.core.Units]
18.96user 0.95system 0:18.39elapsed 108%CPU (0avgtext+0avgdata 947860maxresident)k
1056inputs+1672outputs (17major+203201minor)pagefaults 0swaps
+ for v in "$@"
+ git checkout v2.6.0.2
Note: switching to 'v2.6.0.2'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
HEAD is now at 92a65a3 Merge pull request #509 from NeurodataWithoutBorders/508-remove-international-datestring-parsing
+ echo 'Running using: '
Running using:
+ git describe --tags
v2.6.0.2
+ MATLABPATH=/tmp/matnwb-aH0BDuK/matnwb
+ time matlab -nodesktop -batch 'f='\''../000552/sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb'\''; disp(util.getSchemaVersion(f)); nwb = nwbRead(f)'
2.6.0
nwb =
NwbFile with properties:
nwb_version: '2.6.0'
file_create_date: [1x1 types.untyped.DataStub]
identifier: '19872f12-b3c7-48cb-bc14-f6107c80d9b8'
session_description: 'The incorporation of new information into the hippocampal network is likely to be constrained by its innate architecture and internally generated activity patterns. However, the origin, organization and consequences of such patterns remain poorly understood. In the present study we show that hippocampal network dynamics are affected by sequential neurogenesis. We birthdated CA1 pyramidal neurons with in utero electroporation over 4 embryonic days, encompassing the peak of hippocampal neurogenesis, and compared their functional features in freely moving adult mice. Neurons of the same birthdate displayed distinct connectivity, coactivity across brain states and assembly dynamics. Same-birthdate neurons exhibited overlapping spatial representations, which were maintained across different environments. Overall, the wiring and functional features of CA1 pyramidal neurons reflected a combination of birthdate and the rate of neurogenesis. These observations demonstrate that sequential neurogenesis during embryonic development shapes the preconfigured forms of adult network dynamics.'
session_start_time: 2021-03-19T00:00:00.000000-04:00
timestamps_reference_time: 2021-03-19T00:00:00.000000-04:00
acquisition: [0x1 types.untyped.Set]
analysis: [0x1 types.untyped.Set]
general: [0x1 types.untyped.Set]
general_data_collection: []
general_devices: [1x1 types.untyped.Set]
general_experiment_description: 'Preconfigured dynamics in the hippocampus are guided by embryonic birthdate and rate of neurogenesis'
general_experimenter: [1x1 types.untyped.DataStub]
general_extracellular_ephys: [8x1 types.untyped.Set]
general_extracellular_ephys_electrodes: [1x1 types.hdmf_common.DynamicTable]
general_institution: 'Princeton'
general_intracellular_ephys: [0x1 types.untyped.Set]
general_intracellular_ephys_experimental_conditions: []
general_intracellular_ephys_filtering: []
general_intracellular_ephys_intracellular_recordings: []
general_intracellular_ephys_repetitions: []
general_intracellular_ephys_sequential_recordings: []
general_intracellular_ephys_simultaneous_recordings: []
general_intracellular_ephys_sweep_table: []
general_keywords: [1x1 types.untyped.DataStub]
general_lab: 'Buzsaki'
general_notes: []
general_optogenetics: [0x1 types.untyped.Set]
general_optophysiology: [0x1 types.untyped.Set]
general_pharmacology: []
general_protocol: []
general_related_publications: [1x1 types.untyped.DataStub]
general_session_id: 'e13_16f1_210319'
general_slices: []
general_source_script: []
general_source_script_file_name: []
general_stimulus: []
general_subject: [1x1 types.core.Subject]
general_surgery: []
general_virus: []
intervals: [0x1 types.untyped.Set]
intervals_epochs: [1x1 types.core.TimeIntervals]
intervals_invalid_times: []
intervals_trials: [1x1 types.core.TimeIntervals]
processing: [2x1 types.untyped.Set]
scratch: [0x1 types.untyped.Set]
stimulus_presentation: [0x1 types.untyped.Set]
stimulus_templates: [0x1 types.untyped.Set]
units: [1x1 types.core.Units]
18.51user 0.91system 0:17.87elapsed 108%CPU (0avgtext+0avgdata 928532maxresident)k
8inputs+1640outputs (8major+203498minor)pagefaults 0swaps
+ pwd
/tmp/matnwb-aH0BDuK/matnwb
```
it would be nice if there was a debug log line which provides details at least on matlab invocation here
running dandisets-healthstatus test-files matnwb_nwbRead -- fails
```shell (venv) (dandisets) dandi@drogon:~/cronlib/dandisets-healthstatus$ dandisets-healthstatus test-files matnwb_nwbRead /mnt/backup/dandi/dandisets-healthstatus/dandisets-fuse/000552/sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb 2023-08-09 09:40:58 [DEBUG ] Starting new HTTPS connection (1): api.github.com:443 2023-08-09 09:40:59 [DEBUG ] https://api.github.com:443 "GET /repos/NeurodataWithoutBorders/matnwb/releases/latest HTTP/1.1" 200 842 2023-08-09 09:40:59 [INFO ] Testing /mnt/backup/dandi/dandisets-healthstatus/dandisets-fuse/000552/sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb ... 2023-08-09 09:40:59 [DEBUG ] Using selector: EpollSelector Error using assert Unexpected properties {data_offset}. Your schema version may be incompatible with the file. Consider checking the schema version of the file with `util.getSchemaVersion(filename)` and comparing with the YAML namespace version present in nwb-schema/core/nwb.namespace.yaml Error in types.util.checkUnset (line 17) assert(isempty(dropped),... Error in types.core.SpatialSeries (line 35) types.util.checkUnset(obj, unique(varargin(1:2:end))); Error in io.parseGroup (line 85) parsed = eval([Type.typename '(kwargs{:})']); Error in io.parseGroup (line 38) subg = io.parseGroup(filename, group, Blacklist); Error in io.parseGroup (line 38) subg = io.parseGroup(filename, group, Blacklist); Error in io.parseGroup (line 38) subg = io.parseGroup(filename, group, Blacklist); Error in io.parseGroup (line 38) subg = io.parseGroup(filename, group, Blacklist); Error in nwbRead (line 59) nwb = io.parseGroup(filename, h5info(filename), Blacklist); 2023-08-09 09:51:00 [INFO ] /mnt/backup/dandi/dandisets-healthstatus/dandisets-fuse/000552/sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb: FAIL ```but it is not reporting any detail about version of the matnwb or exact invocation of matlab here, making it impossible to reproduce:
I fail to reproduce when I try with the simpler code/checknwb.sh (but note: that one does not use datalad-fuse -- it downloads the file
```shell (venv) (dandisets) dandi@drogon:~/cronlib/dandisets-healthstatus$ code/checknwb.sh 000552 sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb master v2.6.0.2 /tmp/matnwb-aH0BDuK Cloning into '000552'... remote: Enumerating objects: 1040, done. remote: Counting objects: 100% (1040/1040), done. remote: Compressing objects: 100% (787/787), done. remote: Total 1040 (delta 109), reused 1015 (delta 84), pack-reused 0 Receiving objects: 100% (1040/1040), 182.75 KiB | 2.50 MiB/s, done. Resolving deltas: 100% (109/109), done. Version of the dandiset: 0.230630.2304-1-gad8452b Remote origin not usable by git-annex; setting annex-ignore https://github.com/dandisets/000552/config download failed: Not Found get sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb (from web...) ok (recording state in git...) Cloning into 'matnwb'... remote: Enumerating objects: 9328, done. remote: Counting objects: 100% (2496/2496), done. remote: Compressing objects: 100% (1019/1019), done. remote: Total 9328 (delta 1636), reused 2048 (delta 1472), pack-reused 6832 Receiving objects: 100% (9328/9328), 27.51 MiB | 25.24 MiB/s, done. Resolving deltas: 100% (6007/6007), done. + for v in "$@" + git checkout master Already on 'master' Your branch is up to date with 'origin/master'. + echo 'Running using: ' Running using: + git describe --tags v2.6.0.2-11-g286d6b5 + MATLABPATH=/tmp/matnwb-aH0BDuK/matnwb + time matlab -nodesktop -batch 'f='\''../000552/sub-e13-16f1/sub-e13-16f1_ses-e13-16f1-210319_behavior+ecephys.nwb'\''; disp(util.getSchemaVersion(f)); nwb = nwbRead(f)' 2.6.0 nwb = NwbFile with properties: nwb_version: '2.6.0' file_create_date: [1x1 types.untyped.DataStub] identifier: '19872f12-b3c7-48cb-bc14-f6107c80d9b8' session_description: 'The incorporation of new information into the hippocampal network is likely to be constrained by its innate architecture and internally generated activity patterns. However, the origin, organization and consequences of such patterns remain poorly understood. In the present study we show that hippocampal network dynamics are affected by sequential neurogenesis. We birthdated CA1 pyramidal neurons with in utero electroporation over 4 embryonic days, encompassing the peak of hippocampal neurogenesis, and compared their functional features in freely moving adult mice. Neurons of the same birthdate displayed distinct connectivity, coactivity across brain states and assembly dynamics. Same-birthdate neurons exhibited overlapping spatial representations, which were maintained across different environments. Overall, the wiring and functional features of CA1 pyramidal neurons reflected a combination of birthdate and the rate of neurogenesis. These observations demonstrate that sequential neurogenesis during embryonic development shapes the preconfigured forms of adult network dynamics.' session_start_time: 2021-03-19 timestamps_reference_time: 2021-03-19 acquisition: [0x1 types.untyped.Set] analysis: [0x1 types.untyped.Set] general: [0x1 types.untyped.Set] general_data_collection: '' general_devices: [1x1 types.untyped.Set] general_experiment_description: 'Preconfigured dynamics in the hippocampus are guided by embryonic birthdate and rate of neurogenesis' general_experimenter: [1x1 types.untyped.DataStub] general_extracellular_ephys: [8x1 types.untyped.Set] general_extracellular_ephys_electrodes: [1x1 types.hdmf_common.DynamicTable] general_institution: 'Princeton' general_intracellular_ephys: [0x1 types.untyped.Set] general_intracellular_ephys_experimental_conditions: [] general_intracellular_ephys_filtering: '' general_intracellular_ephys_intracellular_recordings: [] general_intracellular_ephys_repetitions: [] general_intracellular_ephys_sequential_recordings: [] general_intracellular_ephys_simultaneous_recordings: [] general_intracellular_ephys_sweep_table: [] general_keywords: [1x1 types.untyped.DataStub] general_lab: 'Buzsaki' general_notes: '' general_optogenetics: [0x1 types.untyped.Set] general_optophysiology: [0x1 types.untyped.Set] general_pharmacology: '' general_protocol: '' general_related_publications: [1x1 types.untyped.DataStub] general_session_id: 'e13_16f1_210319' general_slices: '' general_source_script: '' general_source_script_file_name: '' general_stimulus: '' general_subject: [1x1 types.core.Subject] general_surgery: '' general_virus: '' intervals: [0x1 types.untyped.Set] intervals_epochs: [1x1 types.core.TimeIntervals] intervals_invalid_times: [] intervals_trials: [1x1 types.core.TimeIntervals] processing: [2x1 types.untyped.Set] scratch: [0x1 types.untyped.Set] stimulus_presentation: [0x1 types.untyped.Set] stimulus_templates: [0x1 types.untyped.Set] units: [1x1 types.core.Units] 18.96user 0.95system 0:18.39elapsed 108%CPU (0avgtext+0avgdata 947860maxresident)k 1056inputs+1672outputs (17major+203201minor)pagefaults 0swaps + for v in "$@" + git checkout v2.6.0.2 Note: switching to 'v2.6.0.2'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -cit would be nice if there was a debug log line which provides details at least on matlab invocation here